Dos Santos, V.F.; Almeida, E.R.; Souza, L.M.P.; Pimentel, A.; Ramdstedt, M.; Soares, T.A. Coarse-Grained Parameters for Simulations of Methyl-Methacrylate-Based Polymer Brushes That Reproduce Experimental Swelling Coefficients. Macromolecules, 2025, ASAP. DOI: 10.1021/acs.macromol.5c00273
Lima, D.C.A.; Bossa, G.V.; Gagliardi, L.; Ciancaglini, P.; Ramos, A.P.; Batista, V.; Soares, T.A. The Effect of Ceramide Ratio on the Membrane Curvature of Mimetic Models of Matrix Vesicles. ACS Physical Chemistry Au, 2025, ASAP. Issue Cover. DOI: 10.1021/acsphyschemau.5c00010
Pantano, S.; Capece, L.; Gagliardi, L.; Merz-Jr., K.M.; Batista, V.; Soares, T. A. Computational Chemistry in the Global South: A Latin American Perspective. J. Chemical Theory and Computation, 2025, v. 21, p. 1507-1508. DOI: 10.1021/acs.jctc.5c00120
Pantano, L. Capece, L. Gagliardi, K. M. Merz Jr., V. Batista, T. A. Soares. Computational Chemistry in the Global South: A Latin American Perspective. Journal of Chemical Information and Modeling, 2025, v. 65, p. 1677-1878. DOI: 10.1021/acs.jcim.5c00148
Gryn’ova, G.; Bereau, T.; Müller, C.; Friederich, P. ; Wade, R.C.; Nunes-Alves, A.; Soares, T.A.; Merz-Jr., K. (2024). Editorial: Chemical Compound Space Exploration by Multiscale High-Throughput Screening and Machine Learning. Journal of Chemical Information and Modeling, v. 64, p. 5737–5738. DOI: 10.1021/acs.jcim.4c01300
Merz-Jr, K. M.; Choong, Y.S.; Cournia, Z.; Isayev, O.; Soares, T. A.; Wei, G.-W.; Zhu, F. (2024) Editorial: Machine Learning in Materials Science. Journal of Chemical Information and Modeling, v. 64, p. 3959–3960. DOI: 10.1021/acs.jcim.4c00727
Karmakar, T.; Soares T.A.; Merz-Jr., K.M. (2024). Enhancing Coarse-Grained Models through Machine Learning. Journal of Chemical Information and Modeling, v. 64, p. 2931–2932. DOI:/10.1021/acs.jcim.4c00537
Frigerio, M.; Freire, R.; Soares, T.A.; Amenitsch, H.; Leser, M.E.; Salentinig, S. (2024) Interfacial Structurization between Triolein and Water from pH and Buffer Ions. Journal of Colloid and Interface Science, v. 665, p. 1091-1101
DOI:10.1016/j.jcis.2024.03.089
Carrer, M.; Eilsø-Nielsen, J.; Cezar, H.M.; Lund, R.; Cascella, M.; Soares, T.A. (2023) Accelerating Lipid Flip-Flop at Low Concentrations: A General Mechanism for Membrane Binding Peptides. Journal of Physical Chemistry Letters, v. 14, p. 7014-7019.
DOI: 10.1021/acs.jpclett.3c01284
Palermo, G.; Soares, T.A. (2023) Editing DNA and RNA through Computations. Journal of Chemical Information and Modeling, v. 63, p. 7603-7604.
Santos, D.E.S.; De Nicola, A.; dos Santos, V.F.; Milano, G.; Soares, T.A. (2023) Exploring the Molecular Dynamics of a Lipid‐A Vesicle at the Atom Level: Morphology and Permeation Mechanism. Journal of Physical Chemistry B. v. 127, p. 6694–6702.
Soares, T.A.; Cournia, Z.; Naidoo, K.; Amaro, R.; Wahab, H.; Merz-Jr, K.M. (2023) Guidelines for Reporting Molecular Dynamics Simulations in JCIM Publications. Journal of Chemical Information and Modeling, v. 63, p. 3227–3229.
Maciel, L.G.; Ferraz, M. V. F.; Oliveira, A.A.; Lins, R.D.; Dos Anjos, J.V.; Guido, R.V.C.; Soares, T.A. (2023) Inhibition of 3-Hydroxykynurenine Transaminase from Aedes aegypti and Anopheles gambiae: A Mosquito-Specific Target to Combat the Transmission of Arboviruses. ACS Bio Med & Chem Au, v. 3, p. 211–222.
DOI:10.1021/acsbiomedchemau.2c00080
Soares, T.A.; Nunes-Alves, A.; Mazzolari, A.; Ruggiu, F.; Wei, G-W.; Merz, K. (2022) The (Re)-Evolution of Quantitative Structure–Activity Relationship (QSAR) Studies Propelled by the Surge of Machine Learning Methods. Journal of Chemical Information and Modeling, v. 62, p. 5317–5320.
Santos, D. E. S.; Coutinho, K.; Soares, T. A. (2022) Surface Assessment Grid Evaluation (SuAVE) for Every Surface Curvature and Cavity Shape. Journal of Chemical Information and Modeling, v. 62, p. 4690–4701. Issue Cover.
Cournia, Z.; Soares, T.A.; Wahab, H.A.; Amaro, R.E. (2022) Celebrating Diversity, Equity, Inclusion, and Respect in Computational and Theoretical Chemistry. Journal of Chemical Information and Modeling,
v. 62, v. 24, p. 6287–6291
Vendite, D. E. S.; Soares, T.A.; Coutinho, K. (2022) The Effect of Surface Composition on the Selective Capture of Atmospheric CO2 by ZIF Nanoparticles: The Case of ZIF8. Journal of Chemical Information and Modeling. v. 62, p. 6530–6543. Issue Cover.
Wei, G.-W.; Soares, T. A.; Wahab, H.A.; Zhu, F. (2022) Editorial: Computational Chemistry in Asia. Journal of Chemical Information and Modeling,
v. 62, p. 5035–5037.
Cascella, M.; Soares, T.A. (2022) Bias Amplification in Gender, Gender Identity, and Geographical Affiliation. Journal of Chemical Information and Modeling, v. 62, p. 6297-6301.
Cournia, Z.; Soares, T.A.; Wahab, H.A.; Amaro, R.E. (2021) Advancing Women in Chemistry. Journal of Chemical Information and Modeling,
v. 61, p. 5305-5306.
Messias, A.; Santos, D. E. S.; Pontes, F. J. S.; Lima, F. S.; Soares, T. A. (2021) The tug of war between Al3+ and Na+ for order-disorder transitions in Lipid-A membranes. Phys. Chem. Chem. Phys., v. 23, p. 15127–15137. DOI:10.1039/D1CP02173G. Selected by PCCP Editors as a 2021 HOT PCCP article.
Wei, G.-W. ; Soares, T. A. ; Wahab, H.A.; Wang, R. (2021) Computational Chemistry in Asia. Journal of Chemical Information and Modeling, v. 61, p. 547-547.
Freire, R. V. M.; Pillco-Valencia, Y.; Da Hora, G. C. A.; Ramstedt, M.; Sandblad, L.; Soares, T. A.; Salentinig, S. (2021) Antimicrobial peptide induced colloidal transformations in bacteria-mimetic vesicles: Combining in silico tools and experimental methods. Journal of Colloid and Interface Science, v. 596, p. 352-363.
DOI: 10.1016/j.jcis.2021.03.060
Maciel, L.; Barbosa, A. S.; De Alencar-Filho, E. B.; Soares, T. A.; Dos Anjos, J. V. (2021) A second Generation of 1,2,4-Oxadiazole Derivatives with Enhanced Solubility for Inhibition of 3-Hydroxykynurenine Transaminase (HKT) from Aedes aegypti. RSC Medicinal Chemistry, v. 12, p. 222-236.
De Nicola, A.; Soares, T. A.; Santos, D. E. S.; Bore, S. L.; Sevink, G. J. A.; Cascella, M.; Milano, G. (2021) Aggregation of Lipid A Variants: a Hybrid Particle-Field Model. Biochimica et Biophysica Acta. v. 1865, p. 129570.
DOI: 10.1016/j.bbagen.2020.129570
Merz, K. M.; Amaro, R.; Cournia, Z. ; Rarey, M.; Soares, T. A. ; Tropsha, A. ; Wahab, H.A.; Wang, R. (2020) Editorial: Method and Data Sharing and Reproducibility of Scientific Results. Journal of Chemical Information and Modeling, v. 60, p. 5868-5869.
Rusu, V. H.; Santos, D. E. S.; Poleto, M. D.; Galheigo, M. M.; Gomes, A. T. A.; Verli, H.; Soares, T. A.; Lins, R. D. (2020) Rotational Profiler: A Fast, Automated, and Interactive Server to Derive Torsional Dihedral Potentials for Classical Molecular Simulation. Journal of Chemical Information and Modeling. v. 60, p. 5923–5927.
Messias, A.; Santos, D. E. S.; Pontes, F. J. S.; Lima, F. S.; Soares, T. A. (2020) Out of Sight, Out of Mind: The Effect of the Equilibration Protocol on the Structural Ensembles of Charged Glycolipid Bilayers. Molecules. v. 25 (21), p 5120-5136. Invited peer-review contribution to special issue Combined Quantum Mechanical and Molecular Mechanical Methods and Simulations II
DOI: 10.3390/molecules25215120
E. Apra, E.J. Bylaska, W.A. De Jong, N. Govind, K. Kowalski, T.P. Straatsma, M. Valiev, H.J.J. van Dam, Y. Alexeev, J.L. Anchell, V. Anisimov, F. Aquino, R. Atta-Fynn, J. Autschbach, N.P. Bauman, J.C. Becca, D.E. Bernholdt, K. Bhaskaran-Nair, S. Bogatko, P. Borowski, J. Boschen, J. Brabec, A. Bruner, E. Cauet, Y. Chen, G.N. Chuev, C. Cramer, J. Daily, M.J.O. Deegan, T.H. Dunning, M. Dupuis, K.G. Dyall, G. Fann, S.A. Fischer, A. Fonari, H. Fruchtl, L. Gagliardi, J. Garza, N. Gawande, S. Ghosh, K. Glaesemann, A.W. Goetz, J. Hammond, V. Helms, E.D. Hermes, K. Hirao, S. Hirata, M. Jacquelin, L. Jensen, B.G. Johnson, H. Jonsson, R.A. Kendall, M. Klemm, R. Kobayashi, V. Konkov, S. Krishnamoorthy, M. Krishnan, Z. Lin, R.D. Lins, R.J. Littlefield, A.J. Logsdail, K. Lopata, W. Ma, A.V. Marenich, J.M. del Campo, D. Mejia-Rodriguez, J.E. Moore, J.M. Mullin, T. Nakajima, D.R. Nascimento, J.A. Nichols, P.J. Nichols, J. Nieplocha, A. Otero-de-la-Roza, B.J. Palmer, A. Panyala, T. Pirojsirikul, B. Peng, R. Peverati, J. Pittner, L. Pollack, R.M. Richard, P. Sadayappan, G.C. Schatz, W.A. Shelton, D. William Silverstein, D.M. Smith, T.A. Soares, D. Song, M. Swart, H.L. Taylor, G. Thomas, V. Tipparaju, D.G. Truhlar, K. Tsemekman, T. Van Voorhis, A. Vazquez-Mayagoitia, P. Verma, O. Villa, A. Vishnu, K. Vogiatzis, D. Wang, J. Weare, M.J. Williamson, T. Windus, K. Wolinski, A.T. Wong, Q. Wu, C. Yang, Q. Yu, M. Zacharias, Z. Zhang, Y. Zhao, R. Harrison. (2020) NWChem: Past, Present, and Future. Journal of Chemical Physics v. 152, p. 184102-184126.
Soares, T.A.; Wahab, H.A. (2020). Outlook on the Development and Application of Molecular Simulations in Latin America. Journal of Chemical Information and Modeling, v. 60, p. 435-438. Editorial for the Special Issue of JCIM on Molecular Simulation in Latin America.
Santos, D. E. S.; Pontes, J. F. S.; Lins, R. D.; Coutinho, K.; Soares, T. A. (2020) SuAVE: A Tool for Analyzing Curvature-Dependent Properties in Chemical Interfaces. Journal of Chemical Information and Modeling, v. 60, p. 473-484.
Maciel, L.G.; Dos Anjos, J.V.; Soares, T.A. (2020) Fast and Low-Cost Evaluation of Hydroxykynurenine Activity. METHODS X, v. 7, p. 100982.
DOI: 10.1016/j.mex.2020.100982
Maciel, L.G.; Oliveira, A.A.; Romão, R.P.; Leal, L.L.L..; Guido, R.V.C.; Silva-Filha, M.H.; dos Anjos, J.V; Soares, T. A. (2020) Discovery of 1,2,4-Oxadiazole Derivatives as a Novel Class of Noncompetitive Inhibitors of 3-Hydroxykynurenine Transaminase (HKT) from Aedes aegypti. Bioorganic and Medicinal Chemistry v. 28, p. 115252-115265.
Soares, T.A.; Wahab, H.A. (2019). Molecular Simulation in Latin America: Coming of Age. Journal of Chemical Information and Modeling, v. 59, p. 3601-3602. Editorial for the Special Issue of JCIM on Molecular Simulation in Latin America.
Capeletti, L. B.; De Oliveira, J. F. A.; Loiola, L. M. D.; Galdino, F. E.; Santos, D. E. S.; Soares, T. A.; Freitas, R. O.; Cardoso, M. B. (2019) Gram‐Negative Bacteria Targeting Mediated by Carbohydrate–Carbohydrate Interactions Induced by Surface‐Modified Nanoparticles. Advanced Functional Materials, v. 29, p. 1904216. Issue Cover.
Yamanaka, T. ; A. De Nicola, A. ; G. Munaò, G. ; Soares, T.A. ; Milano, G. (2019) Effect of the Ligand’s Bulkiness on the Shape of Functionalized Gold Nanoparticles in Aqueous Solutions: A Molecular Dynamics Study. Chemical Physics Letters v. 731, p. 136576-136583.
DOI: 10.1016/j.cplett.2019.07.004
Silva, J. Y. R. ; Proenza, Y. G. ; Da Luz, L. L. ; De Sousa Araújo, S. ; Filho, M. A. G. ; Junior, S. A. ; Soares, Thereza A. ; Longo, R. L. (2019) A Thermo-Responsive Adsorbent-Heater-Thermometer Nanomaterial for Controlled Drug Release: (ZIF-8,EuxTby)@AuNP Core-Shell. Materials Science & Engineering C-Materials for Biological Applications, v. 102, p. 578-588.
DOI: 10.1016/j.msec.2019.04.078
Lima, M. ; Nader, M. ; Santos, D. E. S. ; Soares, T. A. (2019) Compatibility of GROMOS-Derived Atomic Parameters for Lipopolysaccharide Membranes with the SPC/E Water Model and Alternative Long-Range Electrostatic Treatments Using Single Nonbonded Cutoff and Atom-Based Charge Schemes. Journal of the Brazilian Chemical Society, v. 30, p. 2219-2230. Invited peer-review contribution to special issue Brazilian Women in Chemistry
DOI: 10.21577/0103-5053.20190119
Santos, D. E. S. ; Li, D. ; Ramstedt, M. ; Gautrot, J. ; Soares, T. A. (2019) Conformational Dynamics and Responsiveness of Weak and Strong Polyelectrolyte Brushes: Atomistic Simulations of PDMAEMA and PMETAC. Langmuir, v. 35, p. 5037–5049. Issue Cover.
DOI: 10.1021/acs.langmuir.8b04268
Silva-Jr., J.J.; Soares, T.A.; Pol-Fachin, L; Machado, D.C.; Rusu, V. H.; Aguiar, J.P.; Rodrigues, C.G. (2019) Alpha-Hemolysin Nanopore Allows Discrimination of the Microcystin Variants. RSC Advances, v. 9, p. 14683-14691.
Oliveira, I. A. ; Pol-Fachin, L. ; de Carvalho, S. T. ; Lins, R. D. ; Soares T. A.; Mohana-Borges, R. ; Neves, J. L. ; Todeschini, A. R. (2019). Duffy binding-like 1α Adhesin from Plasmodium falciparum Recognizes ABH Histo-Blood Group Saccharide in a Type Specific Manner. Carbohydrate Polymers, v. 207, p. 266-275.
DOI: 10.1016/j.carbpol.2018.11.082
Lorenzon, E. N. ; Nobre, T. M. ; Caseli, L. ; Cilli, E. M. ; Da Hora, G. C. A. ; Soares, T. A. ; Oliveira, O. N. (2018) The “Pre-Assembled State” of Magainin 2 Lysine-Linked Dimer Determines Its Enhanced Antimicrobial Activity. Colloids and Surfaces B: Biointerfaces, v. 167, p. 433-440.
DOI: 10.1016/j.colsurfb.2018.04.034
Paula, M.V. ; Barros, A.L. ; Wanderley, K.A. ; de Sá, G.F. ; Eberlin, M. ; Soares, T.A.; Alves-Jr. S. (2018) Metal Organic Frameworks for Selective Degradation of Amoxicillin in Biomedical Wastes. Journal of the Brazilian Chemical Society, v. 29, p. 2127-2136.
DOI: 10.21577/0103-5053.20180087
Da Silva, J. ; Dias, R. ; Da Hora, G. ; Soares, T.A. ; Meneghetti, M. (2018) Molecular Dynamics Simulations of Cetyltrimethylammonium Bromide (CTAB) Micelles and their Interactions with a Gold Surface in Aqueous Solution. Journal of the Brazilian Chemical Society, v. 29, p. 191-199.
DOI: 10.21577/0103-5053.20170130
Santos, D. E. S. ; Pol-Fachin, L. ; Lins, R. D. ; Soares, T. A. (2017) Polymyxin Binding to the Bacterial Outer Membrane Reveals Cation Displacement and Increasing Membrane Curvature in Susceptible but not in Resistant LPS Chemotypes. Journal of Chemical Information and Modeling, v. 57, p. 2181–2193. Issue Cover.
Silva, L. N. ; Da Hora, G. C. A. ; Soares, T. A. ; Bojer, M. S. ; Ingmer, H. ; Macedo, A. J. ; Trentin, D. S. (2017) Myricetin Protects Galleria mellonella Against Staphylococcus aureus Infection and Inhibits Multiple Virulence Factors. Scientific Reports, v. 7, p. 1-16.
DOI: 10.1038/s41598-017-02712-1
Soares, T. A. ; Vanni, S. ; Milano, G. ; Cascella, M. (2017) Toward Chemically Resolved Computer Simulations of Dynamics and Remodeling of Biological Membranes. Journal of Physical Chemistry Letters, v. 8, p. 3586-3594. (ACS VIDEO on our publication)
DOI: 10.1021/acs.jpclett.7b00493
Bozkurt, E. ; Soares, T. A. ; Rothlisberger, U. (2017) Can Biomimetic Zinc Compounds Assist a (3 + 2) Cycloaddition Reaction? A Theoretical Perspective. Journal of Chemical Theory and Computation, v. 13, p. 6382-6390.
Colak, B. ; Da Silva, J. C. S. ; Soares, T. A. ; Gautrot, J. E. E. (2016) Impact of the Molecular Environment on Thiol–Ene Coupling For Biofunctionalization and Conjugation. Bioconjugate Chemistry, v. 27, p. 2111–2123.
DOI: 10.1021/acs.bioconjchem.6b00349
Da Hora, G. C. A. ; Archilha, N. L. ; Lopes, J. L. S. ; Muller, D. M. ; Cutinho, K. ; Itri, R. ; Soares, T.A. (2016) Membrane Negative Curvature Induced by a Hybrid Peptide from Pediocin PA-1 and Plantaricin 149 as Revealed by Atomistic Molecular Dynamics Simulations. Soft Matter, v. 12, p. 8884-8898.
Cornish, A. J. ; Ginovska, B. ; Thelen, A. ; da Silva, J. C. S. ; Soares, T. A. ; Raugei, S. ; Dupuis, M. ; Shaw, W. J. ; Hegg, E. L. (2016) Single-Amino Acid Modifications Reveal Additional Controls on the Proton Pathway of [FeFe]-Hydrogenase. Biochemistry. v. 55, p 3165-3173.
DOI: 10.1021/acs.biochem.5b01044
Pontes, F. J. S. ; Maia, R. T. ; Lima, M. C. P. ; Ayres, C. F. J. ; Soares, T. A. (2016) The Role of the Conformational Dynamics of Glutathione S-Transferase Epsilon Class on Insecticide Resistance. Journal of the Brazilian Chemical Society, v. 27, 1602-1615.
DOI: 10.5935/0103-5053.20160040
Lorezón, E. N. ; Riske, K. A. ; Troiano, G. F. ; Da Hora, G. C. A. ; Soares, T. A. ; Cilli, E. M. (2016) The Effect of Dimerization on the Mechanism of Action of Aurein 1.2. Biochimica et Biophysica Acta - Biomembranes, v. 1858, p. 1229-1238.
DOI: 10.1016/j.bbamem.2016.02.010
Liu, J. ; Li, X. F. ; Gu, C. Y. ; Da Silva, J. C.S. ; Barros, A. L. ; Júnior, S. A. ; Li, B. H. ; Ren, F. ; Batten, S. R. ; Soares, T. A. (2015) A Combined Experimental and Computational Study of Novel Nanocage-based Metal-Organic Frameworks for Drug Delivery. Dalton Transactions, v. 44, p. 19370-19382.
Dias, R. P. ; Da Hora, G. C.A. ; Ramstedt, M. ; Soares, T. A. (2014) Outer Membrane Remodeling: The Structural Dynamics and Electrostatics of Rough Lipopolysaccharide Chemotypes. Journal of Chemical Theory and Computation, v. 10, p. 2488-2497.
Dias, R. P. ; Li, L. ; Soares, T. A. ; Alexov, E. (2014) Modeling the Electrostatic Potential of Asymmetric Lipopolysaccharide Membranes: The MEMPOT Algorithm Implemented in DelPhi. Journal of Computational Chemistry, v. 35, p. 1418-1429.
Carvalho, P. H. P. R. ; Correa, J. R. ; Guido, B. C. ; Gatto, C. C. ; De'Oliveira, H. C. B. ; Soares, T. A. ; Neto, B. A. D. (2014) Designed Benzothiadiazole Fluorophores for Selective Mitochondrial Imaging and Dynamics. Chemistry - A European Journal, v. 20, p. 15360-15374.
Liu, J. ; WU, J. ; Jia, Z. ; Chen, H. ; Daiguebonne, C.; Guillou, O. ; Sakiyamad, H. ; Soares, T. A. ; Ren, F. ; NG, S. W. ; Li, Q. (2014) Two Isoreticular Metal-Organic Frameworks with CdSO4-like Topology: Selective Gas Sorption and Drug Delivery. Dalton Transactions, v. 43, p. 17265-17273.
Mota, A. A. R. ; Carvalho, P. H. P. R. ; Guido, B. C. ; Oliveira, H. C. B. ; Soares, T. A. ; Correa, J. R. ; Neto, B. A. D. (2014) Bioimaging, Cellular Uptake and Dynamics in Living Cells of a Lipophilic Fluorescent Benzothiadiazole at Low Temperature (4 °C). Chemical Science, v. 5, p. 3995-4003.
Ravi, H. K. ; Stach, M. ; Soares, T. A. ; Darbre, T. ; Reymond, J. L. ; Cascella, M. (2013). Electrostatics and Flexibility Drive Membrane Recognition and Early Penetration by Antimicrobial Peptide Dendrimer bH1. Chemical Communications, v. 49, p. 8821-8823.
Nascimento Jr., A. ; Pontes, F. J. S. ; Lins, R. D. ; Soares, T. A. (2013). Hydration, Ionic Valence and Cross-Linking Propensities of Cations Determine the Stability of Lipopolysaccharide Membranes. Chemical Communications, v. 50, p. 231-233.
Alvim, H. G. O. ; Fagg, E. L. ; de Oliveira, A. L. ; de Oliveira, H. C. B. ; Freitas, S. M. ; Xavier, M. A. E. ; Soares, T. A. ; Gomes, A. F. ; Gozzo, F. C. ; Silva, W. ; Neto, B. A. D. (2013) Probing Deep into the Interaction of a Fluorescent Chalcone Derivative and Bovine Serum Albumin (BSA): An Experimental and Computational Study. Organic and Biomolecular Chemistry, v. 11, p. 4764-4777.
Ravi, H. K. ; Stach, M. ; Soares, T. A. ; Darbre, T. ; Reymond, Jean-Louis; Cascella, M. (2013) Electrostatics and Flexibility Drive Membrane Recognition and Early Penetration by Antimicrobial Peptide Dendrimer bH1. Chemical Communications. v. 49, p. 8821-8823, 2013.
Viana, I. F. T. ; Soares, T. A. ; Lima, L. F. O. ; Marques, E. T. A. ; Krieger, M. ; Dhalia, R. ; Lins, R. D. (2013) De Novo Design of Immunoreactive Conformation-specific HIV-1 Epitopes Based on Top7 Scaffold. RSC Advances, v. 3, p. 11790-11800.
Soares, T. A. ; Oliveira, V. S. ; Pimenteira, C. ; Da Silva-Alves, D. C. B. ; Leal, L. L. L. ; Neves-Filho, R. A. W. ; Navarro, D. M. A. F. ; Santos, G. K. N. ; Dutra, K. A. ; Dos Anjos, J. V. (2013) The Enzyme 3-Hydroxykynurenine Transaminase as Potential Target for 1,2,4-oxadiazoles with Larvicide Activity Against the Dengue Vector Aedes aegypti. Bioorganic and Medicinal Chemistry, v. 21, p. 6996-7003.
DOI: 10.1016/j.bmc.2013.09.020
Kirschner, K. N. ; Lins, R. D. ; Maass, A. ; Soares, T. A. (2012) A GLYCAM-based Force Field for Simulations of Lipopolysaccharide Membranes: Parametrization and Validation. Journal of Chemical Theory and Computation, v. 8, p. 4719–4731.
Vasconcelos I.B. ; Silva, T. ; Milito, G. ; Soares, T. A. ; Rodrigues, M. O. ; Costa Jr, N. B. ; Freire, R. O. ; Alves Jr, S. (2012) Cytotoxicity and Slow Release of the Anti-Cancer Drug Doxorubicin from ZIF-8. RSC Advances, v. 2, p. 9437-9442.
Pontes, F. J. S. ; Rusu, V. H. ; Soares, T. A. ; Lins, R. D. (2012) The effect of Temperature, Cations and Number of Acyl Chains on the Lamellar to Non-Lamellar Transition in Lipid-A Membranes: A Microscopic View. Journal of Chemical Theory and Computation, v. 8, p. 3830–3838.
de Paula, M. V. ; Rodrigues, M. O. ; Wanderley, K. A. ; Vasconcelos, I. B. ; Alves Jr, S. ; Soares, T. A. (2012) Metal Organic Frameworks for Drug Delivery and Environmental Remediation: A Molecular Docking Approach. International Journal Quantum Chemistry, v. 112, p. 3346-3355.
Gomes, D. E. B. ; Lins, R. D. ; Pascutti, P. G. ; Lei, C. ; Soares, T. A. (2011) Conformational Variability of Organophosphorous Hydrolase upon Soman and Paraoxon Binding, Journal of Physical Chemistry B, v. 115, p. 15389-15398.
Gomes, D. E. B. ; Lins, R. D. ; Pascutti, P. G. ; Lei, C. ; Soares, T. A. (2010) The Role of nonbonded interactions in the conformational dynamics of organophosphorous hydrolase adsorbed onto functionalized sílica surfaces, Journal of Physical Chemistry B, v. 114, p. 513-540.
Soares, T. A. ; Boschek, C. B. ; Apiyo, D. ; Baird, C. ; Straatsma, T. P. (2010) Molecular basis of the structural stability of a Top7-based scaffold at extreme pH and temperature conditions.Journal of Molecular Graphics and Modelling, v. 28, p. 755-765.
DOI: 10.1016/j.jmgm.2010.01.013
Chen, L. T. L. ; Yao, Q. ; Soares, T. A. ; Squier, T. C. ; Bigelow, D. J. (2009) Phospholamban Modulates the Functional Coupling between Nucleotide Domains in Ca-ATPase Oligomeric Complexes in Cardiac Sarcoplasmic Reticulum. Biochemistry, v. 48, p. 2411-2421.
Straatsma, T. P. ; Soares, T. A. (2009) Characterization of the outer membrane protein OprF of Pseudomonas aeruginosa in a lipopolysaccharide membrane by computer simulation. Proteins, v. 74, p. 475-488.
DOI: 10.1002/prot.22165
Apiyo, D. O. ; Soares, T. A. ; Engelmann, H. E. ; Pefaur, N. B. ; Straatsma, T. P. ; Baird, C. L. (2009) Engineering an ultra-stable affinity reagent based on Top7. Protein Engineering, Design and Selection, v. 22, p. 325-332.
Soares, T. A. ; Straatsma, T. P. (2008) Assessment of the convergence of molecular dynamics simulations of lipopolysaccharide membranes. Molecular Simulation, v. 34, p. 295-307.
DOI: 10.1080/08927020701829880
Lei, C. ; Soares, T. A. ; Shin, Y. ; Liu, J. ; Ackerman, E.J. (2008) Enzyme specific activity in functionalized nanoporous supports. Nanotechnology, v. 19, p. 125102.
DOI: 10.1088/0957-4484/19/12/125102
Gomes D.E.B. ; Lins R.D. ; Pascutti P.G. ; Straatsma T.P. ; Soares, T.A. (2008) Molecular Models to Emulate Confinement Effects on the Internal Dynamics of Organophosphorous Hydrolase, Lecture Notes in Bioinformatics, v. 5167, p. 68-78.
DOI: 10.1007/978-3-540-85557-6_7
Peterson E.S. ; Williams L. ; Stephan E.G. ; Rose S. ; Corrigan A. ; Lai C. ; Lins R.D. ; Critchlow T. ; Straatsma T.P. ; Soares T.A. ; Scarberry R. (2008) Northwest Trajectory Analysis Capability: A Platform for Enhancing Computational Biophysics Analysis, In Proceedings of the 2008 International Conference on Bioinformatics and Computational Biology, BIOCOMP 2008, pp. 558-562. CSREA Press, Bogart, GA
Soares T.A., Straatsma T.P., and Lins R.D. (2008) Influence of the B-band O-antigen chain in the Structure and Electrostatics of the Lipopolysaccharide Membrane of Pseudomonas aeruginosa, Journal of Brazilian Chemical Society, v. 19, p. 312-320 (invited contribution in honor to the 80th birthday of Prof. R. C. Ferreira). Invited peer-review contribution to special issue dedicated to the 80th Birthday of Prof. Ricardo Ferreira
DOI: 10.1590/S0103-50532008000200018
Soares, T. A. ; Osman, M.A. ; Straatsma, T.P. (2007) Molecular Dynamics of Organophosphorous Hydrolases Bound to the Nerve Agent Soman. Journal of Chemical Theory and Computation, v. 3, p. 1569-1579.
Soares, T.A. ; Hünenberger, P.H. ; Kastenholtz, M. ; Krautler, V. ; Lenz T. ; Lins, R.D. ; Oostenbrink, C. ; van Gunsteren, WF. (2005) Development of a Consistent Nucleic Acid Parameter Set for the GROMOS Force Field, Journal of Computational Chemistry, v. 26, p. 725-737.
Oostenbrink, C. ; Soares, T. A. ; Vegt, N. F. A. ; van Gunsteren, W.F. (2005) Validation of the 53A6 GROMOS force field. European Biophysics Journal, v. 34, p. 273-284.
DOI: 10.1007/s00249-004-0448-6
Soares, T.A. ; Daura, X.; Oostenbrink, C. ; Smith, L. J. ; van Gunsteren, W. F. (2004). Validation of the GROMOS force-field parameter set 45A3 against nuclear magnetic resonance data of hen egg lysozyme. Journal of Biomolecular NMR, v. 30, p. 407-422, 2004.
DOI: 10.1007/s10858-004-5430-1
Soares, T. ; Christen, M. ; Hu, K ; van Gunsteren, W.F. (2004) Alpha- and beta-polypeptides show a different stability of helical secondary structure. Tetrahedron. v. 60, p. 7775 - 7780.
DOI: 10.1016/j.tet.2004.06.062
Soares, T. A. ; Ferreira, R. (2004) Applications of the Poisson-Boltzmann equation to the calculation of pH-dependent properties in proteins. Química Nova. v. 27, p. 640 - 647.
DOI: 10.1590/S0100-40422004000400019
Mustata, G.I. ; Soares, T. A.; Briggs, J.M. (2003) Molecular dynamics studies of alanine racemase: A structural model for drug design. Biopolymers. v. 70, p.186 - 200.
Soares, T.A. ; Lins, R.D. ; Straatsma, T.P. ; Briggs, J.M. (2002) Internal dynamics and ionization states of the macrophage migration inhibitory factor: Comparison between wild-type and mutant forms. Biopolymers, v. 65, p. 313-323.
van Gunsteren, W. F. ; Soares, T. A. et al. (2001) Molecular dynamics simulation of biomolecular systems. Chimia. v. 55, p. 856 - 860.
Soares, T. A. ; Straatsma, T.P. ; Miller, J. H. (2001) Revisiting the structural flexibility of the complex p21(ras)-GTP: The catalytic conformation of the molecular switch II. Proteins. v. 45, p. 297 - 312.
Soares, T. A. (2001) Women in science and technology: Restricted success. Química Nova. v. 24, p. 281 - 285.
DOI: 10.1590/S0100-40422001000200020
Lins, R.D. ; Adesokan, A.A. ; Soares, T.A ; Briggs, J.M. (2000) Investigations On Human Immunodeficiency Virus Type-1 Integrase/DNA Binding Interactions via Molecular Dynamics and Electrostatics Calculations.Pharmacology and Therapeutics, v. 85, p. 123-131.
DOI: 10.1016/S0163-7258(99)00059-5
Soares, T. A. ; Goodsell, D. S., Ferreira, R. ; Olson, A. J. ; Briggs, J.M. (2000) Ionization state and molecular docking studies for the macrophage migration inhibitory factor: the role of lysine 32 in the catalytic mechanism. Journal of Molecular Recognition, v. 13, p. 146 - 156.
DOI: 10.1002/1099-1352(200005/06)13:3<146::AID-JMR497>3.0.CO;2-4
Soares, T. A.; Goodsell, D. S. ; Briggs, J.M. ; Ferreira, R. ; Olson, A. J. (1999) Docking of 4-oxalocrotonate tautomerase substrates: Implications for the catalytic mechanism. Biopolymers, v. 50, p. 319 - 328.
DOI: 10.1002/(SICI)1097-0282(199909)50:3<319::AID-BIP7>3.0.CO;2-8
Lins, R.D. ; Soares, T.A. ; Ferreira, R. ; Longo R. (1999) Solvent Access to Aspartyl and Succinimidyl residues in the Amyloid 1-28 beta peptide. Zeitschrift für Naturforschung, v. 54c, p. 264-270.
Lins, R.D. ; Soares, T.A. ; Ferreira R. (1998) Unusual Kinetic Pathway for the Prebiotic Oligomerization of Ribonucleic Acids Explains the Monochirality of the Polyribotides. Anais da Academia Brasileira de Ciências, v. 70, p. 423-428.
Soares; T.A. ; Lins, R.D. ; Longo, R. ; Garratt, R. ; Ferreira, R. (1997) Plural Origins of Molecular Homochirality in our Biota, PartII. The Relative Stabilities of Homochiral and Mixed Oligoribotides and Peptides. Zeitschrift für Naturforschung, v. 52c, p. 89-96.
Lins, R.D. ; Soares, T.A. ; Ferreira, R. (1996) Plural Origins of Molecular Homochirality in our Biota. Zeitschrift für Naturforschung, v. 51c, p.70-74.
Soares, T.A. 1996. Introduction to the study of the ribozymes. Brazilian Society of Genetics Publisher. São Paulo, Brazil. 200 p. (BOOK)
Soares, T.A. ; Lins R.D. (1995) Ribozymes - not every enzyme is a protein. Quimica Nova,
v. 18, p. 375-378. http://quimicanova.sbq.org.br/imagebank/pdf/Vol18No4_375_v18_n4_09.pdf
Soares, T. A. ; Garratt, R. ; Ferreira, R. . Estudos Por Simulacao Computacional de Alfa-Helices Formadas Por Aminoacidos D/L.. Anais da Academia Brasileira de Ciências (Impresso), Brasil, v. 66, n.3, p. 393-393, 1994.